Variant report

Variant	rs11654606
Chromosome Location	chr17:59788895-59788896
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:59777901..59779551-chr17:59787087..59789823,2	MCF-7	breast:
2	chr17:59788127..59788947-chr17:59800069..59800999,2	MCF-7	breast:
3	chr17:56736402..56738017-chr17:59788439..59790142,2	MCF-7	breast:
4	chr17:59787823..59789456-chr17:59835997..59838639,2	MCF-7	breast:
5	chr17:59780675..59785135-chr17:59787206..59790127,5	MCF-7	breast:
6	chr17:59787606..59790047-chr17:59879549..59882493,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000202077	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11079451	0.91[CHB][hapmap];0.81[JPT][hapmap];0.96[YRI][hapmap];0.85[ASN][1000 genomes]
rs11079454	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11867566	0.82[ASN][1000 genomes]
rs11871785	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2007931	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2040609	0.87[CHB][hapmap]
rs2106663	0.93[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2158005	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2159451	0.85[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35090865	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35524448	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4988357	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56218811	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62071871	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62071872	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6504065	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67223644	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7214703	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7219555	0.85[ASN][1000 genomes]
rs7220740	0.85[ASN][1000 genomes]
rs7222482	0.91[CHB][hapmap];0.87[JPT][hapmap];0.83[YRI][hapmap];0.86[ASN][1000 genomes]
rs8064683	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9908115	0.91[CHB][hapmap];0.82[JPT][hapmap];0.85[ASN][1000 genomes]
rs9912366	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9915787	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9916780	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3378293	chr17:59744117-60124899	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv908673	chr17:59767501-59926645	Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11654606	VEZF1	cis	parietal	SCAN
rs11654606	RNF43	cis	parietal	SCAN
rs11654606	AKAP1	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59763400-59792800	Weak transcription	NH-A	brain
2	chr17:59766000-59819000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr17:59767600-59792800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr17:59767600-59793200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr17:59771800-59794600	Weak transcription	HSMM	muscle
6	chr17:59778200-59805800	Weak transcription	Thymus	Thymus
7	chr17:59779400-59790000	Weak transcription	HepG2	liver
8	chr17:59780000-59793400	Weak transcription	Fetal Heart	heart
9	chr17:59780400-59791000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr17:59780800-59793000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr17:59781000-59791800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr17:59781600-59835400	Weak transcription	Hela-S3	cervix
13	chr17:59782800-59793200	Weak transcription	Fetal Lung	lung
14	chr17:59783000-59793600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr17:59783200-59790200	Weak transcription	A549	lung
16	chr17:59783400-59793200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr17:59783800-59793600	Weak transcription	Fetal Intestine Large	intestine
18	chr17:59784000-59794600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr17:59784200-59793000	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr17:59784400-59792800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr17:59784400-59793400	Weak transcription	NHEK	skin
22	chr17:59784400-59815200	Weak transcription	HMEC	breast
23	chr17:59785000-59790400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr17:59785000-59793400	Weak transcription	K562	blood
25	chr17:59785200-59794400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr17:59785600-59791600	Strong transcription	Dnd41	blood
27	chr17:59786200-59790400	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr17:59786200-59790600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr17:59786400-59792800	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr17:59786400-59793600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr17:59786600-59790400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr17:59786600-59792800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr17:59786600-59792800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr17:59786600-59792800	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr17:59786600-59794400	Weak transcription	Fetal Stomach	stomach
36	chr17:59786600-59815400	Weak transcription	Fetal Thymus	thymus
37	chr17:59786800-59792600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr17:59787000-59790400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr17:59787200-59790400	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr17:59787200-59792800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr17:59787200-59793800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr17:59787400-59792000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr17:59788600-59790600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr17:59788600-59792800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr17:59788800-59789800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr17:59788800-59791000	Weak transcription	GM12878-XiMat	blood
47	chr17:59788800-59791400	Weak transcription	Primary hematopoietic stem cells	blood

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